Neanderthal Woman's Genome Reveals Unknown Human Lineage

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The existence of a mysterious ancient human lineage and the
genetic changes that separate modern humans from their closest
extinct relatives are among the many secrets now revealed in the
first high-quality genome sequence from a Neanderthal woman,
researchers say.

The
Neanderthal woman whose toe bone was sequenced also reveals
inbreeding may have been common among her recent ancestors, as
her parents were closely related, possibly half-siblings or
another near relation.

Although modern humans are the world's only surviving human
lineage, others also once lived on Earth. These included
Neanderthals, the closest extinct relatives of modern humans,
and the relatively newfound
Denisovans, whose
genetic footprint apparently extended from Siberia to the
Pacific islands of Oceania. Both Neanderthals and Denisovans
descended from a group that diverged from the ancestors of all
modern humans. [ See
Photos of Neanderthal Bone & Denisovan Fossils ]

The first signs of Denisovans came from a finger bone and a molar
tooth discovered in Denisova Cave in southern Siberia in 2008. To
learn more about Denisovans, scientists examined a woman's toe
bone, which was unearthed in the cave in 2010 and showed physical
features resembling those of both Neanderthals and modern humans.
The fossil is thought to be about 50,000 years old, and slightly
older than previously analyzed Denisovan fossils.

Human interbreeding

The scientists focused mostly on the fossil's nuclear DNA, the
genetic material from the chromosomes in the nucleus of the cell
that a person receives from both their mother and father. They
also examined the genome of this fossil's mitochondria — the
powerhouses of the cell, which possess their own DNA and get
passed down solely from the mother.

The investigators completely sequenced the fossil's nuclear DNA,
with each position (or nucleotide) sequenced an average of 50
times. This makes the sequence's quality at least as high as that
of genomes sequenced from present-day people.

The genetic analysis revealed the toe bone belonged to a
Neanderthal. When compared with other Neanderthal mitochondrial
DNA samples, this newfound fossil's closest known relatives are
Neanderthals found in Mezmaiskaya Cave in the Caucasus Mountains
about 2,100 miles (3,380 kilometers) away.

These findings helped the scientists refine the
human family tree, further confirming that different human
lineages interbred. They estimated about 1.5 to 2.1 percent of
DNA of people outside Africa are Neanderthal in origin, while
about 0.2 percent of DNA of mainland Asians and Native Americans
is Denisovan in origin.

"Admixture seems to be common among human groups," said study
lead author Kay Prüfer, a computational geneticist at the Max
Planck Institute for Evolutionary Anthropology in Leipzig,
Germany.

Intriguingly, the scientists discovered that apparently Denisovans
interbred with an unknown human lineage, getting as much as
2.7 to 5.8 percent of their genomes from it. This mystery
relative apparently split from the ancestors of all modern
humans, Neanderthals and Denisovans between 900,000 years and 4
million years ago, before these latter groups started diverging
from each other.

This enigmatic lineage could even potentially be Homo
erectus, the earliest undisputed predecessor of modern
humans. There are no signs this unknown group interbred with
modern humans or Neanderthals, Prüferadded. [ The
10 Biggest Mysteries of the First Humans ]

"Some unknown archaic DNA might have caught a ride through time
by living on in Denisovans until we dug the individual up and
sequenced it," Prüfertold LiveScience. "It opens up the prospect
to study the sequence of an archaic (human lineage) that might be
out of reach for DNA sequencing."

Interbreeding took place between Neanderthals and Denisovans as
well. These new findings suggest at least 0.5 percent of the
Denisovan genome came from Neanderthals. However, nothing of the
Denisovan genome has been detected in Neanderthals so far.

In addition, "the age of the Neanderthals and Denisovans we
sequenced also doesn't allow us to say whether any gene flow from
modern humans to Neanderthals or Denisovans happened," Prüfer
said. The Neanderthals and Denisovans that researchers have
sequenced the DNA of to date "probably lived at a time when no
modern humans were around," he explained.

Modern humans' distinguishing features

It remains uncertain when modern humans, Neanderthals and
Denisovans diverged from one another. The researchers currently
estimate modern humans split from the common ancestors of all
Neanderthals and Denisovans between 550,000 and 765,000 years
ago, and Neanderthals and Denisovans diverged from each other
between 381,000 and 473,000 years ago.

Genetic analysis revealed the parents of the woman whose toe bone
they analyzed were closely related — possibly half-siblings, or
an uncle and niece, or an aunt and nephew, or a grandfather and
granddaughter, or a grandmother and grandson. Inbreeding among
close relatives was apparently common among the woman's recent
ancestors. It remains uncertain as to whether inbreeding was some
kind of cultural practice among these Neanderthals or whether it
was unavoidable due to how few Neanderthals apparently lived in
this area, Prüfer said.

By comparing modern human, Neanderthal and
Denisovan genomes, the researchers identified more than
31,000 genetic changes that distinguish modern humans from
Neanderthals and Denisovans. These changes may be linked with the
survival and success of modern humans — a number have to do with
brain
development.

"If one speculates that we modern humans carry some genetic
changes that enabled us to develop technology to the degree we
did and settle in nearly all habitable areas on the planet, then
these must be among those changes," Prüfer said. "It is hard to
say what exactly these changes do, if anything, and it will take
the next few years to find out whether hidden among all these
changes are some that helped us modern humans to develop
sophisticated technology and settle all over the planet."

Prüfer and his colleagues detailed their findings in the Dec. 19
issue of the journal Nature.